[English] 日本語
Yorodumi
- PDB-1oby: Crystal structure of the complex of PDZ2 of syntenin with a synde... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1oby
TitleCrystal structure of the complex of PDZ2 of syntenin with a syndecan-4 peptide.
Components
  • SYNDECAN-4
  • SYNTENIN 1
KeywordsCELL ADHESION / ADHESION-COMPLEX / PDZ DOMAIN / SIGNAL TRANSDUCTION / NUCLEAR PROTEIN
Function / homology
Function and homology information


regulation of fibroblast migration / Defective B3GALT6 causes EDSP2 and SEMDJL1 / Defective B4GALT7 causes EDS, progeroid type / Defective B3GAT3 causes JDSSDHD / Defective EXT2 causes exostoses 2 / Defective EXT1 causes exostoses 1, TRPS2 and CHDS / Glycosaminoglycan-protein linkage region biosynthesis / interleukin-5 receptor complex / HS-GAG biosynthesis / interleukin-5 receptor binding ...regulation of fibroblast migration / Defective B3GALT6 causes EDSP2 and SEMDJL1 / Defective B4GALT7 causes EDS, progeroid type / Defective B3GAT3 causes JDSSDHD / Defective EXT2 causes exostoses 2 / Defective EXT1 causes exostoses 1, TRPS2 and CHDS / Glycosaminoglycan-protein linkage region biosynthesis / interleukin-5 receptor complex / HS-GAG biosynthesis / interleukin-5 receptor binding / inner ear receptor cell stereocilium organization / positive regulation of extracellular exosome assembly / Neurofascin interactions / syndecan binding / HS-GAG degradation / substrate-dependent cell migration, cell extension / positive regulation of exosomal secretion / cytoskeletal adaptor activity / costamere / ureteric bud development / negative regulation of receptor internalization / frizzled binding / Ephrin signaling / protein targeting to membrane / RIPK1-mediated regulated necrosis / neural tube closure / Syndecan interactions / thrombospondin receptor activity / positive regulation of transforming growth factor beta receptor signaling pathway / RSV-host interactions / fibronectin binding / Respiratory syncytial virus (RSV) attachment and entry / positive regulation of phosphorylation / positive regulation of focal adhesion assembly / negative regulation of T cell proliferation / positive regulation of stress fiber assembly / positive regulation of epithelial to mesenchymal transition / Retinoid metabolism and transport / phosphatidylinositol-4,5-bisphosphate binding / lysosomal lumen / protein kinase C binding / Cell surface interactions at the vascular wall / wound healing / regulation of mitotic cell cycle / adherens junction / protein sequestering activity / positive regulation of JNK cascade / Golgi lumen / Regulation of necroptotic cell death / actin cytoskeleton organization / azurophil granule lumen / melanosome / cell migration / positive regulation of cell growth / nuclear membrane / extracellular vesicle / chemical synaptic transmission / blood microparticle / cytoskeleton / Attachment and Entry / intracellular signal transduction / positive regulation of cell migration / membrane raft / protein heterodimerization activity / focal adhesion / positive regulation of cell population proliferation / Neutrophil degranulation / synapse / endoplasmic reticulum membrane / negative regulation of transcription by RNA polymerase II / cell surface / : / extracellular exosome / extracellular region / nucleoplasm / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Syndecan / Syndecan, conserved site / Syndecans signature. / Syndecan/Neurexin domain / Syndecan domain / Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif / : / PDZ domain / Pdz3 Domain ...Syndecan / Syndecan, conserved site / Syndecans signature. / Syndecan/Neurexin domain / Syndecan domain / Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif / : / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Syntenin-1 / Syndecan-4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsKang, B.S. / Cooper, D.R. / Devedjiev, Y. / Derewenda, U. / Derewenda, Z.S.
CitationJournal: Structure / Year: 2003
Title: Molecular Roots of Degenerate Specificity in Syntenin'S Pdz2 Domain: Reassessment of the Pdz Recognition Paradigm
Authors: Kang, B.S. / Cooper, D.R. / Devedjiev, Y. / Derewenda, U. / Derewenda, Z.S.
History
DepositionJan 31, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Oct 16, 2019Group: Data collection / Other / Category: pdbx_database_status / reflns
Item: _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs
Revision 1.5Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SYNTENIN 1
B: SYNTENIN 1
P: SYNDECAN-4
Q: SYNDECAN-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5657
Polymers18,2774
Non-polymers2883
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)58.337, 54.441, 50.219
Angle α, β, γ (deg.)90.00, 98.65, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2034-

HOH

-
Components

#1: Protein SYNTENIN 1 / SYNDECAN BINDING PROTEIN 1 / MELANOMA DIFFERENTIATION ASSOCIATED PROTEIN-9 / MDA-9 / SCAFFOLD ...SYNDECAN BINDING PROTEIN 1 / MELANOMA DIFFERENTIATION ASSOCIATED PROTEIN-9 / MDA-9 / SCAFFOLD PROTEIN PBP1 / TACIP18 / PRO-TGF-ALPHA CYTOPLASMIC DOMAIN-INTERACTING PROTEIN 18


Mass: 8394.598 Da / Num. of mol.: 2 / Fragment: PDZ2, RESIDUES 197-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O00560
#2: Protein/peptide SYNDECAN-4 / AMPHIGLYCAN / SYND4 / RYUDOCAN CORE PROTEIN


Mass: 743.761 Da / Num. of mol.: 2 / Fragment: LAST 6 RESIDUES, RESIDUES 193-198 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P31431
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMOL_ID 1: FUNCTIONS AS AN ADAPTER PROTEIN. MAY ALSO FUNCTION TO COUPLE SYNDECANS TO CYTOSKELETAL ...MOL_ID 1: FUNCTIONS AS AN ADAPTER PROTEIN. MAY ALSO FUNCTION TO COUPLE SYNDECANS TO CYTOSKELETAL TRANSCRIPTION PROTEINS OR SIGNALING COMPONENTS. ALSO SEEMS TO COUPLE FACTOR SOX4 TO THE IL-5 RECEPTOR (IL5RA) MOL_ID 2: CELL SURFACE PROTEOGLYCAN CONTAINING HEPARAN SULFATE

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 49.7 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.8
Details: SITTING DROP WITH 0.1 M HEPES, PH 6.8, 1.6 M AMMONIUM SULFATE, 20 MM COCL2, AND 0.2 MGSO4
Crystal grow
*PLUS
Temperature: 294 K / pH: 6.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails (eV)Chemical formula
10.1 MHEPES1reservoirpH6.8
21.6 Mammonium sulfate1reservoir
320 mM1reservoirCoCl2
40.2 M1reservoirMgSO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.97946
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 31, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 46421 / % possible obs: 97.4 % / Redundancy: 3.57 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 25.8
Reflection shellResolution: 1.85→1.92 Å / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 2.86 / % possible all: 83.7
Reflection
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 50 Å / Num. obs: 12987 / Num. measured all: 46421 / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
% possible obs: 83.7 % / Num. unique obs: 1108 / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 2.86

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N99

1n99


Resolution: 1.85→49.39 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.645 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.226 985 7.6 %RANDOM
Rwork0.175 ---
obs-12001 97.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 16.42 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20 Å2-0.68 Å2
2--0.44 Å20 Å2
3----1.7 Å2
Refinement stepCycle: LAST / Resolution: 1.85→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1212 0 15 145 1372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211235
X-RAY DIFFRACTIONr_bond_other_d0.0010.021118
X-RAY DIFFRACTIONr_angle_refined_deg1.8151.9461663
X-RAY DIFFRACTIONr_angle_other_deg0.94132610
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7625156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1130.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021342
X-RAY DIFFRACTIONr_gen_planes_other0.0150.02222
X-RAY DIFFRACTIONr_nbd_refined0.2040.2227
X-RAY DIFFRACTIONr_nbd_other0.2570.21273
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.2732
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2470.296
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.6680.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3660.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2510.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.121.5787
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.00521275
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.163448
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.0054.5388
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.336 55
Rwork0.259 739
Refinement TLS params.

T33: 0.0164 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.32040.596-1.75432.7056-0.61484.8398-0.0471-0.0468-0.0891-0.1466-0.0233-0.0417-0.17670.16820.07050.08390.0029-0.00460.10130.00438.5350.03311.409
21.1031-0.63781.20351.819-0.66514.9443-0.0677-0.03250.02110.0309-0.1043-0.04750.27790.09630.1720.1082-0.00290.04120.10330.00748.83930.56312.219
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A197 - 270
2X-RAY DIFFRACTION2B197 - 270
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.012
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.82

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more